Re: Topology and parameters for nitrate and nitrite ion

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon Jul 01 2013 - 02:52:28 CDT

Then you're in luck; OPLS parameters for small molecules with no rotatable
bonds often perform well when transferred to CHARMM, because the CHARMM
nonbonded parameters are historically based on OPLS ones. Disclaimer: this
is true of no other force field than OPLS!

On 07/01/2013 03:39 AM, amin_at_imtech.res.in wrote:
> Sadly, I didn't find any CHARMM parameters for nitrate or nitrite in the
> literature. I did find amber and opls parameters for nitrate but not for
> nitrite. As you are actively involved in CHARMM development I would request you
> to consider these two ions whenever possible as these ions are really important
> in biological systems.
>
> Warm Regards.
> Amin.
>
>
>> So you didn't find anything in the literature, then? Because that's where
>> most people get their small ion parameters in practice. It would surprise
>> me if nobody made an attempt at parameterizing nitrate before...
>>
>> Also, I'd like to emphasize that if you only want to have the ion present
>> in an active site, and are not interested in studying binding/unbinding,
>> then even a very crude model just might be good enough. I'm in the group
>> that is responsible for the majority of the official CHARMM force field
>> development, and even we have on occasion knowingly used a very crude and
>> imperfect model for an active site ion. (Did I mention ions are
>> difficult?) I believe we even needed distance restraints to keep the darn
>> thing in place (not sure at all, it wasn't my project). As long as you
>> fully realize it's a crude model and you interpret and present your
>> results accordingly, I would say it's OK. That's the pragmatic side of things.
>>
>>
>> On 07/01/2013 12:00 AM, amin_at_imtech.res.in wrote:
>>> Thanks for the detailed answer. Actually I had followed the swissparam
>>> approach
>>> a few days ago. But reading your earlier post made me realize that this may
>>> not
>>> be an accurate way of doing it. Overall it looks too specialized a job for me
>>> to
>>> attempt. Hoping some person with the required skill set will do this in near
>>> future.
>>>
>>> Regards.
>>> Amin.
>>>
>>>
>>>> - small anorganic ions usually require special dedicated L-J parameters.(*)
>>>>
>>>> - as far as I know, CHARMM does not officially have L-J parameters for
>>>> nitrate and nitrite.
>>>>
>>>> - Swissparam uses the L-J parameters from the official CHARMM release so
>>>> it doesn't have them either. Hence, it cannot be expected to do a good job
>>>> at this assignment.(+)
>>>>
>>>> - Charges that are directly derived from QM calculations generally cannot
>>>> be combined with the CHARMM L-J parameters; see:
>>>> http://mackerell.umaryland.edu/~kenno/cgenff/faq.html#esp
>>>> A relevant 3rd party study illustrating this point is
>>>> A. Ahmed, S. I. Sandler; J. Chem. Theory Comput. 2013, 9 (6), 2774–2785
>>>>
>>>> - 3rd party nitrate and nitrite parameter sets that claim to be
>>>> compatible with CHARMM may be found in the literature. Their degree of
>>>> actual CHARMM compatibility and their quality may vary widely. Depending
>>>> on your purpose, they may or may not be good enough for you. If you
>>>> require the ion to remain bound in an enzyme active site, quality is less
>>>> critical than if you plan to allow it to unbind. To gauge the quality,
>>>> look for MD validation runs using the TIP3P water model, aiming to
>>>> reproduce solution-phase experimental data that are relevant for your
>>>> purpose.
>>>>
>>>> Cheers,
>>>>
>>>> Kenno.
>>>>
>>>> (*) Parameterization of small anorganic ions is extremely specialized
>>>> work, requiring (among other things) the calculation of Radial
>>>> Distribution Functions of different salt solutions and comparison with
>>>> experiment. Usually, in the additive force field, special NBFIX terms are
>>>> required for correct solution-phase behavior in the presence of different
>>>> counterions. Within the CHARMM community, the authority on ion
>>>> parametrization is Benoît Roux; see his work.
>>>>
>>>> (+) More generally spoken, the Swissparam approach of combining CHARMM L-J
>>>> parameters with MMFF94 charges and dihedrals is flawed; see my post of a
>>>> few days ago. The Swissparam developers advertise their work as a tool for
>>>> obtaining very rough models for large-scale virtual screening, not for
>>>> detailed MD studies.
>>>>
>>>>
>>>>
>>>> On 06/30/2013 03:02 PM, flavio seixas wrote:
>>>>> Hi,
>>>>>
>>>>> Download the *.mol2 version of nitrite and nitrate molecules from zinc
>>>>> database: *zinc*.docking.org/
>>>>> Special attention to protonated state of molecules at pH 7.0 (or other
>>>>> desired pH).
>>>>> Submit each of them to www.*swissparam*.ch/
>>>>>
>>>>> Download toppar and param files in Charmm format (*.zip).
>>>>>
>>>>> If you want accurate force fields, optimize molecules with
>>>>> B3LYP/6-31G++(d,p) level of theory and replace partial charges at toppar
>>>>> files generated by Swissparam.
>>>>>
>>>>> Regards,
>>>>> -------------------------------------
>>>>> Flavio Augusto Vicente Seixas
>>>>> Laboratory of Structural Biochemistry
>>>>> Department of Biochemistry
>>>>> Universidade Estadual de Maringá, PR, Brazil
>>>>> http://www.uem.br
>>>>> --------------------------------------------------------------------------
>>>>> *From:* "amin_at_imtech.res.in" <amin_at_imtech.res.in>
>>>>> *To:* namd-l_at_ks.uiuc.edu
>>>>> *Sent:* Saturday, June 29, 2013 2:51 PM
>>>>> *Subject:* namd-l: Topology and parameters for nitrate and nitrite ion
>>>>>
>>>>> Dear NAMD users,
>>>>> I want to run a simulation of a protein with bound nitrite and nitrate
>>>>> ions. Can
>>>>> someone please guide me on how/where to obtain the topology and parameter
>>>>> files
>>>>> for these ions? Any suggestions will be highly appreciated.
>>>>>
>>>>> Regards.
>>>>> Amin.
>>>>>
>>>>> ______________________________________________________________________
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>>>>
>>>>
>>>
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>>
>>
>
>
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202
>

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